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comparison rg_rnaStar.xml @ 1:bc685d13b637 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
author iuc
date Thu, 19 Nov 2015 05:34:06 -0500
parents b2326241bb09
children ace9f5a2b40f
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0:b2326241bb09 1:bc685d13b637
1 <tool id="rna_star" name="rnastar" version="2.4.0d"> 1 <tool id="rna_star" name="RNA STAR" version="2.4.0d">
2 <description>Gapped-read mapper for RNA-seq data</description> 2 <description>Gapped-read mapper for RNA-seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.4.0d">rnastar</requirement> 4 <requirement type="package" version="2.4.0d">rnastar</requirement>
5 <requirement type="package" version="0.1.19">samtools</requirement> 5 <requirement type="package" version="0.1.19">samtools</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
9 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
10 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
8 <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/> 11 <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/>
9 </stdio> 12 </stdio>
10 13
11 <command> 14 <command><![CDATA[
12 ## 15 ##
13 ## Run STAR. 16 ## Run STAR.
14 ## 17 ##
15 #if str($refGenomeSource.genomeSource) == 'history': 18 #if str($refGenomeSource.genomeSource) == 'history':
16 mkdir -p tempstargenomedir; STAR --runMode genomeGenerate --genomeDir "tempstargenomedir" --genomeFastaFiles "$refGenomeSource.ownFile" --runThreadN 2 19 mkdir -p tempstargenomedir; STAR --runMode genomeGenerate --genomeDir "tempstargenomedir" --genomeFastaFiles "$refGenomeSource.ownFile" --runThreadN 2
32 #end if 35 #end if
33 --readFilesIn $singlePaired.input1 36 --readFilesIn $singlePaired.input1
34 #if str($singlePaired.sPaired) == "paired" 37 #if str($singlePaired.sPaired) == "paired"
35 $singlePaired.input2 38 $singlePaired.input2
36 #end if 39 #end if
37 --runThreadN 4 40 --runThreadN \${GALAXY_SLOTS:-4}
38 #if str($params.settingsType) == "full": 41 #if str($params.settingsType) == "full":
39 --chimSegmentMin $params.chim_segment_min 42 --chimSegmentMin $params.chim_segment_min
40 --chimScoreMin $params.chim_score_min 43 --chimScoreMin $params.chim_score_min
44 --seedSearchStartLmax $params.seed_search_start_l_max
45 --alignSJDBoverhangMin $params.align_sjdb_overhang_min
46 --outFilterScoreMinOverLread $params.out_filter_score_min_over_l_read
41 #end if 47 #end if
42 48
43 ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools. 49 ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools.
44 $outSAMstrandField $outFilterIntronMotifs $outSAMattributes 50 $outSAMstrandField $outFilterIntronMotifs $outSAMattributes
45 51
47 ## 53 ##
48 ## BAM conversion. 54 ## BAM conversion.
49 ## 55 ##
50 56
51 ## Convert aligned reads. 57 ## Convert aligned reads.
52 samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2&gt;/dev/null 58 samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null
53 59
54 ## Convert chimeric reads. 60 ## Convert chimeric reads.
55 #if str($params.settingsType) == "full" and $params.chim_segment_min > 0: 61 #if str($params.settingsType) == "full" and $params.chim_segment_min > 0:
56 ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2&gt;/dev/null 62 ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2>/dev/null
57 #end if 63 #end if
58 </command> 64 ]]></command>
59 65
60 <inputs> 66 <inputs>
61 <param name="jobName" type="text" size="120" value="rna-star run" label="Job narrative (added to output names)" 67 <param name="jobName" type="text" value="rna-star run" label="Job narrative (added to output names)"
62 help="Only letters, numbers and underscores (_) will be retained in this field"> 68 help="Only letters, numbers and underscores (_) will be retained in this field">
63 <sanitizer invalid_char=""> 69 <sanitizer invalid_char="">
64 <valid initial="string.letters,string.digits"><add value="_" /> </valid> 70 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
65 </sanitizer> 71 </sanitizer>
66 </param> 72 </param>
107 </param> 113 </param>
108 <param name="outSAMstrandField" type="select" label="Include extra sam attributes for downstream processing"> 114 <param name="outSAMstrandField" type="select" label="Include extra sam attributes for downstream processing">
109 <option value="--outSAMstrandField intronMotif" selected="true">Add XS for cufflinks</option> 115 <option value="--outSAMstrandField intronMotif" selected="true">Add XS for cufflinks</option>
110 <option value="">No XS added to sam output</option> 116 <option value="">No XS added to sam output</option>
111 </param> 117 </param>
112 <param name="outFilterIntronMotifs" type="select" label="Canonical junction preparation for unstranded data"> 118 <param name="outFilterIntronMotifs" type="select" label="Canonical junction preparation for unstranded data (--outFilterIntronMotifs)">
113 <option value="">No special handling - all non-canonical junctions passed through</option> 119 <option value="">No special handling - all non-canonical junctions passed through</option>
114 <option value="--outFilterIntronMotifs RemoveNoncanonical" selected="true">Remove all non-canonical junctions for eg cufflinks</option> 120 <option value="--outFilterIntronMotifs RemoveNoncanonical" selected="true">Remove all non-canonical junctions for eg cufflinks</option>
115 <option value="--outFilterIntronMotifs RemoveNoncanonicalUnannotated">Remove only unannotated non-canonical junctions for eg cufflinks</option> 121 <option value="--outFilterIntronMotifs RemoveNoncanonicalUnannotated">Remove only unannotated non-canonical junctions for eg cufflinks</option>
116 </param> 122 </param>
117 <!-- Parameter settings. --> 123 <!-- Parameter settings. -->
120 <option value="preSet" selected="true">Use Defaults</option> 126 <option value="preSet" selected="true">Use Defaults</option>
121 <option value="full">Full parameter list</option> 127 <option value="full">Full parameter list</option>
122 </param> 128 </param>
123 <when value="preSet" /> 129 <when value="preSet" />
124 <!-- Full/advanced params. --> 130 <!-- Full/advanced params. -->
125 <when value="full"> 131 <when value="full">
126 <param name="chim_segment_min" type="integer" min="0" value="0" label="Minimum chimeric segment length" /> 132 <param name="chim_segment_min" type="integer" min="0" value="0" label="Minimum chimeric segment length (--chimSegmentMin)" />
127 <param name="chim_score_min" type="integer" min="0" value="0" label="Minimum total (summed) score of the chimeric segments" /> 133 <param name="chim_score_min" type="integer" min="0" value="0" label="Minimum total (summed) score of the chimeric segments (--chimScoreMin)" />
128 134 <param name="seed_search_start_l_max" type="integer" min="0" value="50" label="Defines the search start point through the read - the read is split into pieces no longer than this value (--seedSearchStartLmax)" />
135 <param name="align_sjdb_overhang_min" type="integer" value="1" label="Minimum overhang for annotated junctions (--alignSJDBoverhangMin)" />
136 <param name="out_filter_score_min_over_l_read" type="float" value="0.66" label="OutFilterScoreMin normalized to read length; sum of mates’ lengths for paired-end reads (--outFilterScoreMinOverLread)" />
129 </when> 137 </when>
130 </conditional> 138 </conditional>
131 </inputs> 139 </inputs>
132 140
133 <outputs> 141 <outputs>
214 </actions> 222 </actions>
215 </data> 223 </data>
216 </outputs> 224 </outputs>
217 <tests> 225 <tests>
218 <test> 226 <test>
219 <param name='input1' value='tophat_in2.fastqsanger' ftype='fastqsanger' /> 227 <param name='input1' value='tophat_in2.fastqsanger' ftype='fastqsanger' />
220 <param name='jobName' value='rnastar_test' /> 228 <param name='jobName' value='rnastar_test' />
221 <param name='genomeSource' value='history' /> 229 <param name='genomeSource' value='history' />
222 <param name='ownFile' value='tophat_test.fa' /> 230 <param name='ownFile' value='tophat_test.fa' />
223 <param name='sPaired' value='single' /> 231 <param name='sPaired' value='single' />
224 <param name='outSAMattributes' value='--outSAMattributes All' /> 232 <param name='outSAMattributes' value='--outSAMattributes All' />
225 <param name='outSAMstrandField' value='--outSAMstrandField intronMotif' /> 233 <param name='outSAMstrandField' value='--outSAMstrandField intronMotif' />
226 <param name='outFilterIntronMotifs' value='--outFilterIntronMotifs RemoveNoncanonical' /> 234 <param name='outFilterIntronMotifs' value='--outFilterIntronMotifs RemoveNoncanonical' />
227 <output name='output_log' file='rnastar_test.log' compare='diff' lines_diff = '10'/> 235
228 <output name='splice_junctions' file="rnastar_test_splicejunctions.bed" compare="sim_size" delta="200"/> 236 <output name='output_log' file='rnastar_test.log' compare='diff' lines_diff = '10'/>
229 <output name='mapped_reads' file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" /> 237 <output name='splice_junctions' file="rnastar_test_splicejunctions.bed"/>
238 <output name='mapped_reads' file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" />
239 </test>
240 <test>
241 <param name='input1' value='tophat_in2.fastqsanger' ftype='fastqsanger' />
242 <param name='jobName' value='rnastar_test' />
243 <param name='genomeSource' value='history' />
244 <param name='ownFile' value='tophat_test.fa' />
245 <param name='sPaired' value='single' />
246 <param name='outSAMattributes' value='--outSAMattributes All' />
247 <param name='outSAMstrandField' value='--outSAMstrandField intronMotif' />
248 <param name='outFilterIntronMotifs' value='--outFilterIntronMotifs RemoveNoncanonical' />
249
250 <param name="settingsType" value="full" />
251
252 <param name="chim_segment_min" value="0" />
253 <param name="chim_score_min" value="0" />
254 <param name="seed_search_start_l_max" value="25" />
255 <param name="align_sjdb_overhang_min" value="3" />
256 <param name="out_filter_score_min_over_l_read" value="0.9" />
257
258 <output name='output_log' file='rnastar_test2.log' compare='diff' lines_diff = '10'/>
259 <output name='splice_junctions' file="rnastar_test2_splicejunctions.bed"/>
260 <output name='mapped_reads' file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />
230 </test> 261 </test>
231 </tests> 262 </tests>
232 <help> 263 <help>
233
234 **What it does** 264 **What it does**
235 Runs the rna star gapped aligner. Suited to paired or single end rna-seq. 265 Runs the rna star gapped aligner. Suited to paired or single end rna-seq.
236 266
237 8.2: SAM alignments 267 8.2: SAM alignments
238 268
289 canonical junctions will be kept. 319 canonical junctions will be kept.
290 320
291 321
292 **Attributions** 322 **Attributions**
293 323
294 Note that each component has its own license. Good luck with figuring out your obligations. 324 Note that each component has its own license:
325 - RNA STAR: GPLv3
326 - samtools: MIT/Expat License
295 327
296 rna_star - see the web site at rna_star_ 328 rna_star - see the web site at rna_star_
297 329
298 For details, please see the rna_starMS_ 330 For details, please see the rna_starMS_
299 "STAR: ultrafast universal RNA-seq aligner" 331 "STAR: ultrafast universal RNA-seq aligner"
307 and odds and ends of other code and documentation comprising this tool was 339 and odds and ends of other code and documentation comprising this tool was
308 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts 340 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts
309 341
310 .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml 342 .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
311 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/ 343 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
312 .. _rna_star: http://code.google.com/p/rna-star/ 344 .. _rna_star: https://github.com/alexdobin/STAR
313 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full 345 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
314 .. _Galaxy: http://getgalaxy.org 346 .. _Galaxy: http://getgalaxy.org
315 347
316 </help> 348 </help>
317 <citations> 349 <citations>
318 <citation type="doi">doi: 10.1093/bioinformatics/bts635</citation> 350 <citation type="doi">10.1093/bioinformatics/bts635</citation>
319 </citations> 351 </citations>
320 </tool> 352 </tool>
321 353